The studies presented in this manuscript address the diversity and ecology of prokaryotic communities in anoxic zones of two pelagic lake ecosystems: the Lake Aydat typically eutrophic, which presents a period of thermal stratification anoxic hypolimnion, and Lake Pavin, unique meromictic lake in France, showing an area permanently anoxic. The analyzes of the structure, diversity, and spatial dynamics-and / or temporal bacterioplankton anoxic strata of these two lakes by molecular approaches have revealed high microbial diversity enhanced by spatial stratification of bacterioplankton. Further investigations on phylogenetic relationships and the study of microbial metabolism have focused on communities in the anoxic zone of Lake Pavin because of its original character. The clone libraries constructed from samples anoxic water taken at different strata in the monimolimnion revealed that bacterial communities are dominated by species affiliated to δ-Proteobacteria, to Verrucomicrobia, Bacteroidetes and the candidate division OP11. The sequences of 16S rRNA Archaea are mainly affiliated to the group of Methanosarcinales, an observation confirmed by in situ hybridization. In vitro studies of dissimilatory reduction of Fe (III), in cultures of enrichment, confirmed that high concentrations of ferrous iron observed in the sub-chemocline of Lake Pavin resulted partly from the activity of microorganisms. In these enrichments, microorganisms couple the reduction of Fe (III) with the preferential oxidation of fumarate, H2, CH4, and lactate. No accumulation of Fe (II) was observed in the enrichments supplemented with acetate as the electron donor. This observation suggests that this metabolite could be mainly used in the process of methanogenesis, and could be produced in part by the activity of gram-positive bacteria homoacétogènes. The heterogeneity of TTGE profiles made from the different conditions of enhancements WCR suggests that they may occupy very different ecological niches in the monimolimnion of Lac Pavin. No sequence was affiliated with the WCR * Required identified in other ecosystems. The affiliation of sequences in species of the genus Suggests that some SRB Desulfovibrio † use this electron acceptor. Activities Significant reduction of Fe (III) were also identified in strains fermentative isolated from the anoxic zone of the lake. The more specific study of the strain BS2 has revealed that this pathway could confer an advantage and therefore environmentally friendly energy. All the work that lies in the field of microbial ecology and environment opens a wide field of investigation as applied to the cognitive level. The provide opportunities to refine the understanding of the role of anaerobic microorganisms lake systems in biogeochemical cycles and more generally in understanding the role of microbial biodiversity in order to respond in a reasoned way to a societal demand strong in these areas.
